https://github.com/bids-apps/SPM

BIDS App containing an instance of the SPM software.
https://github.com/bids-apps/SPM

bids bidsapp spm

Last synced: 2 days ago
JSON representation

BIDS App containing an instance of the SPM software.

• Host: GitHub
• URL: https://github.com/bids-apps/SPM
• Owner: bids-apps
• License: apache-2.0
• Created: 2016-08-02T15:47:06.000Z (over 8 years ago)
• Default Branch: master
• Last Pushed: 2024-04-30T09:47:16.000Z (7 months ago)
• Last Synced: 2024-08-03T13:14:22.338Z (3 months ago)
• Topics: bids, bidsapp, spm
• Language: MATLAB
• Homepage: https://hub.docker.com/r/bids/spm/tags
• Size: 77.1 KB
• Stars: 14
• Watchers: 8
• Forks: 12
• Open Issues: 11
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

• awesome-bids - SPM

README

        
# SPM BIDS App

## Description

[BIDS App](http://bids-apps.neuroimaging.io/) containing an instance of the [SPM12 software](http://www.fil.ion.ucl.ac.uk/spm/).

## Documentation

Extensive documentation can be found in the [SPM manual](http://www.fil.ion.ucl.ac.uk/spm/doc/manual.pdf).

## Usage

To launch an instance of the container and analyse some data in BIDS format, type:

```bash

$ docker run bids/spm bids_dir output_dir level [--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]] [--config CFG_FILE]

```

For example, to run an analysis in ```participant``` level mode, type:

```bash

$ docker run -ti --rm \

  -v /tmp:/tmp \

  -v /var/tmp:/var/tmp \

  -v /path/to/local/bids/input/dataset/:/data \

  -v /path/to/local/output/:/output \

  bids/spm \

  /data /output participant --participant_label 01

```

For example, to run an analysis in ```group``` level mode with a user-defined pipeline, type:

```bash

$ docker run -ti --rm \

  -v /tmp:/tmp \

  -v /var/tmp:/var/tmp \

  -v /path/to/local/bids/input/dataset/:/data \

  -v /path/to/local/output/:/output \

  -v /path/to/local/cfg/:/cfg \

  bids/spm \

  /data /output group --config /cfg/my_pipeline_group.m

```

To build the container, type:

```bash

$ docker build -t /spm12 .

```

### Configuration file

The configuration file is a MATLAB script detailing the analysis pipeline to be executed. Two struct variables, ```BIDS``` and ```BIDS_App``` are available from within the script, containing details from the command line and the BIDS-formatted dataset. In particular, the ```BIDS``` structure can be queried using the ```spm_BIDS()``` function (see [this](https://en.wikibooks.org/wiki/SPM/BIDS)). The default configuration files for first and second level analyses are ```pipeline_participant.m``` and ```pipeline_group.m```. A template for a single configuration file for all levels could be as follow:

```bash

if strcmp(BIDS_App.level,'participant')

    % First level analysis

    % Get T1-weighted image filename for given subject:

    % a = spm_BIDS(BIDS,'data', 'modality','anat', 'type','T1w');

    % ...

else

    % Second level analysis

    % The name of the directory containing first level outputs is stored in:

    % BIDS_App.outdir

    % ...

end

```

## Error Reporting

If you have a specific problem with the SPM BIDS App, please open an [issue](https://github.com/BIDS-Apps/SPM/issues) on GitHub.

If your issue concerns SPM more generally, please use the [SPM mailing list](https://www.jiscmail.ac.uk/cgi-bin/webadmin?A0=spm).

## Acknowledgement

Please refer to:

```

@Book{spm,

  editor = {K.J. Friston and J. Ashburner and S.J. Kiebel and T.E. Nichols and W.D. Penny},

  title = {Statistical Parametric Mapping: The Analysis of Functional Brain Images},

  publisher = {Academic Press},

  year = {2007},

  url = {http://store.elsevier.com/product.jsp?isbn=9780123725608}

}

```